rs6882716

Variant names:

• chr5-10797774-G-A
• rs6882716

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.786 in 152,120 control chromosomes in the GnomAD database, including 48,954 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.79 (48954 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119500 AN: 152002 Hom.: 48934 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.786

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.786 AC: 119561 AN: 152120 Hom.: 48954 Cov.: 32 AF XY: 0.778 AC XY: 57864 AN XY: 74384

African (AFR) AF: 0.690 AC: 28614 AN: 41466

American (AMR) AF: 0.732 AC: 11186 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2877 AN: 3468

East Asian (EAS) AF: 0.140 AC: 724 AN: 5184

South Asian (SAS) AF: 0.643 AC: 3102 AN: 4822

European-Finnish (FIN) AF: 0.869 AC: 9213 AN: 10604

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.899 AC: 61121 AN: 67984

Other (OTH) AF: 0.778 AC: 1644 AN: 2112

Alfa AF: 0.840 Hom.: 13300

Bravo AF: 0.769

Asia WGS AF: 0.419 AC: 1459 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.56
DANN	Benign	0.50
PhyloP100		-0.27

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6882716; hg19: chr5-10797886;